Methylation: Addition of methyl groups. In histo-chemistry methylation is used to esterify carboxyl groups and remove sulfate groups by treating tissue sections with hot methanol in the presence of hydrochloric acid. (From Stedman, 25th ed)DNA Methylation: Addition of methyl groups to DNA. DNA methyltransferases (DNA methylases) perform this reaction using S-ADENOSYLMETHIONINE as the methyl group donor.CpG Islands: Areas of increased density of the dinucleotide sequence cytosine--phosphate diester--guanine. They form stretches of DNA several hundred to several thousand base pairs long. In humans there are about 45,000 CpG islands, mostly found at the 5' ends of genes. They are unmethylated except for those on the inactive X chromosome and some associated with imprinted genes.Genome: The genetic complement of an organism, including all of its GENES, as represented in its DNA, or in some cases, its RNA.Epigenesis, Genetic: A genetic process by which the adult organism is realized via mechanisms that lead to the restriction in the possible fates of cells, eventually leading to their differentiated state. Mechanisms involved cause heritable changes to cells without changes to DNA sequence such as DNA METHYLATION; HISTONE modification; DNA REPLICATION TIMING; NUCLEOSOME positioning; and heterochromatization which result in selective gene expression or repression.DNA (Cytosine-5-)-Methyltransferase: An enzyme that catalyzes the transfer of a methyl group from S-ADENOSYLMETHIONINE to the 5-position of CYTOSINE residues in DNA.Sulfites: Inorganic salts of sulfurous acid.Genome, Human: The complete genetic complement contained in the DNA of a set of CHROMOSOMES in a HUMAN. The length of the human genome is about 3 billion base pairs.Promoter Regions, Genetic: DNA sequences which are recognized (directly or indirectly) and bound by a DNA-dependent RNA polymerase during the initiation of transcription. Highly conserved sequences within the promoter include the Pribnow box in bacteria and the TATA BOX in eukaryotes.Cytosine: A pyrimidine base that is a fundamental unit of nucleic acids.Sequence Analysis, DNA: A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.5-Methylcytosine: A methylated nucleotide base found in eukaryotic DNA. In ANIMALS, the DNA METHYLATION of CYTOSINE to form 5-methylcytosine is found primarily in the palindromic sequence CpG. In PLANTS, the methylated sequence is CpNpGp, where N can be any base.Genomic Imprinting: The variable phenotypic expression of a GENE depending on whether it is of paternal or maternal origin, which is a function of the DNA METHYLATION pattern. Imprinted regions are observed to be more methylated and less transcriptionally active. (Segen, Dictionary of Modern Medicine, 1992)Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.Genome, Bacterial: The genetic complement of a BACTERIA as represented in its DNA.Genome-Wide Association Study: An analysis comparing the allele frequencies of all available (or a whole GENOME representative set of) polymorphic markers in unrelated patients with a specific symptom or disease condition, and those of healthy controls to identify markers associated with a specific disease or condition.Azacitidine: A pyrimidine analogue that inhibits DNA methyltransferase, impairing DNA methylation. It is also an antimetabolite of cytidine, incorporated primarily into RNA. Azacytidine has been used as an antineoplastic agent.DNA Modification Methylases: Enzymes that are part of the restriction-modification systems. They are responsible for producing a species-characteristic methylation pattern, on either adenine or cytosine residues, in a specific short base sequence in the host cell's own DNA. This methylated sequence will occur many times in the host-cell DNA and remain intact for the lifetime of the cell. Any DNA from another species which gains entry into a living cell and lacks the characteristic methylation pattern will be recognized by the restriction endonucleases of similar specificity and destroyed by cleavage. Most have been studied in bacterial systems, but a few have been found in eukaryotic organisms.Genome, Viral: The complete genetic complement contained in a DNA or RNA molecule in a virus.Gene Silencing: Interruption or suppression of the expression of a gene at transcriptional or translational levels.Molecular Sequence Data: Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.Epigenomics: The systematic study of the global gene expression changes due to EPIGENETIC PROCESSES and not due to DNA base sequence changes.Histones: Small chromosomal proteins (approx 12-20 kD) possessing an open, unfolded structure and attached to the DNA in cell nuclei by ionic linkages. Classification into the various types (designated histone I, histone II, etc.) is based on the relative amounts of arginine and lysine in each.Genome, Plant: The genetic complement of a plant (PLANTS) as represented in its DNA.Methyltransferases: A subclass of enzymes of the transferase class that catalyze the transfer of a methyl group from one compound to another. (Dorland, 28th ed) EC 2.1.1.Polymerase Chain Reaction: In vitro method for producing large amounts of specific DNA or RNA fragments of defined length and sequence from small amounts of short oligonucleotide flanking sequences (primers). The essential steps include thermal denaturation of the double-stranded target molecules, annealing of the primers to their complementary sequences, and extension of the annealed primers by enzymatic synthesis with DNA polymerase. The reaction is efficient, specific, and extremely sensitive. Uses for the reaction include disease diagnosis, detection of difficult-to-isolate pathogens, mutation analysis, genetic testing, DNA sequencing, and analyzing evolutionary relationships.Long Interspersed Nucleotide Elements: Highly repeated sequences, 6K-8K base pairs in length, which contain RNA polymerase II promoters. They also have an open reading frame that is related to the reverse transcriptase of retroviruses but they do not contain LTRs (long terminal repeats). Copies of the LINE 1 (L1) family form about 15% of the human genome. The jockey elements of Drosophila are LINEs.Gene Expression Profiling: The determination of the pattern of genes expressed at the level of GENETIC TRANSCRIPTION, under specific circumstances or in a specific cell.DNA: A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).Magnetic Resonance Imaging: Non-invasive method of demonstrating internal anatomy based on the principle that atomic nuclei in a strong magnetic field absorb pulses of radiofrequency energy and emit them as radiowaves which can be reconstructed into computerized images. The concept includes proton spin tomographic techniques.Dinucleoside Phosphates: A group of compounds which consist of a nucleotide molecule to which an additional nucleoside is attached through the phosphate molecule(s). The nucleotide can contain any number of phosphates.DNA-Cytosine Methylases: Methylases that are specific for CYTOSINE residues found on DNA.Brain Mapping: Imaging techniques used to colocalize sites of brain functions or physiological activity with brain structures.Polymorphism, Single Nucleotide: A single nucleotide variation in a genetic sequence that occurs at appreciable frequency in the population.Genomics: The systematic study of the complete DNA sequences (GENOME) of organisms.Oligonucleotide Array Sequence Analysis: Hybridization of a nucleic acid sample to a very large set of OLIGONUCLEOTIDE PROBES, which have been attached individually in columns and rows to a solid support, to determine a BASE SEQUENCE, or to detect variations in a gene sequence, GENE EXPRESSION, or for GENE MAPPING.Phylogeny: The relationships of groups of organisms as reflected by their genetic makeup.Histone-Lysine N-Methyltransferase: An enzyme that catalyzes the methylation of the epsilon-amino group of lysine residues in proteins to yield epsilon mono-, di-, and trimethyllysine. EC 18.104.22.168.Chromosome Mapping: Any method used for determining the location of and relative distances between genes on a chromosome.Models, Genetic: Theoretical representations that simulate the behavior or activity of genetic processes or phenomena. They include the use of mathematical equations, computers, and other electronic equipment.Cluster Analysis: A set of statistical methods used to group variables or observations into strongly inter-related subgroups. In epidemiology, it may be used to analyze a closely grouped series of events or cases of disease or other health-related phenomenon with well-defined distribution patterns in relation to time or place or both.RNA, Long Noncoding: A class of untranslated RNA molecules that are typically greater than 200 nucleotides in length and do not code for proteins. Members of this class have been found to play roles in transcriptional regulation, post-transcriptional processing, CHROMATIN REMODELING, and in the epigenetic control of chromatin.Antelopes: Any of various ruminant mammals of the order Bovidae. They include numerous species in Africa and the American pronghorn.Phenotype: The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.DNA, Neoplasm: DNA present in neoplastic tissue.Image Processing, Computer-Assisted: A technique of inputting two-dimensional images into a computer and then enhancing or analyzing the imagery into a form that is more useful to the human observer.Chromatin: The material of CHROMOSOMES. It is a complex of DNA; HISTONES; and nonhistone proteins (CHROMOSOMAL PROTEINS, NON-HISTONE) found within the nucleus of a cell.Deoxyribonuclease HpaII: One of the Type II site-specific deoxyribonucleases (EC 22.214.171.124). It recognizes and cleaves the sequences C/CGG and GGC/C at the slash. HpaII is from Haemophilus parainfluenzae. Several isoschizomers have been identified. EC 3.1.21.-.S-Adenosylmethionine: Physiologic methyl radical donor involved in enzymatic transmethylation reactions and present in all living organisms. It possesses anti-inflammatory activity and has been used in treatment of chronic liver disease. (From Merck, 11th ed)Algorithms: A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.Lysine: An essential amino acid. It is often added to animal feed.Genetic Loci: Specific regions that are mapped within a GENOME. Genetic loci are usually identified with a shorthand notation that indicates the chromosome number and the position of a specific band along the P or Q arm of the chromosome where they are found. For example the locus 6p21 is found within band 21 of the P-arm of CHROMOSOME 6. Many well known genetic loci are also known by common names that are associated with a genetic function or HEREDITARY DISEASE.Transcription, Genetic: The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.Gene Expression Regulation, Neoplastic: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in neoplastic tissue.Gene Expression Regulation: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control (induction or repression) of gene action at the level of transcription or translation.Support Vector Machines: Learning algorithms which are a set of related supervised computer learning methods that analyze data and recognize patterns, and used for classification and regression analysis.Computational Biology: A field of biology concerned with the development of techniques for the collection and manipulation of biological data, and the use of such data to make biological discoveries or predictions. This field encompasses all computational methods and theories for solving biological problems including manipulation of models and datasets.Alleles: Variant forms of the same gene, occupying the same locus on homologous CHROMOSOMES, and governing the variants in production of the same gene product.Genome, Fungal: The complete gene complement contained in a set of chromosomes in a fungus.Genes, p16: Tumor suppressor genes located on human chromosome 9 in the region 9p21. This gene is either deleted or mutated in a wide range of malignancies. (From Segen, Current Med Talk, 1995) Two alternatively spliced gene products are encoded by p16: CYCLIN-DEPENDENT KINASE INHIBITOR P16 and TUMOR SUPPRESSOR PROTEIN P14ARF.Mutation: Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations.Protein Methyltransferases: Enzymes that catalyze the methylation of amino acids after their incorporation into a polypeptide chain. S-Adenosyl-L-methionine acts as the methylating agent. EC 2.1.1.snRNP Core Proteins: The protein components that constitute the common core of small nuclear ribonucleoprotein particles. These proteins are commonly referred as Sm nuclear antigens due to their antigenic nature.Brain: The part of CENTRAL NERVOUS SYSTEM that is contained within the skull (CRANIUM). Arising from the NEURAL TUBE, the embryonic brain is comprised of three major parts including PROSENCEPHALON (the forebrain); MESENCEPHALON (the midbrain); and RHOMBENCEPHALON (the hindbrain). The developed brain consists of CEREBRUM; CEREBELLUM; and other structures in the BRAIN STEM.Pattern Recognition, Automated: In INFORMATION RETRIEVAL, machine-sensing or identification of visible patterns (shapes, forms, and configurations). (Harrod's Librarians' Glossary, 7th ed)Cell Line: Established cell cultures that have the potential to propagate indefinitely.Cell Line, Tumor: A cell line derived from cultured tumor cells.Genotype: The genetic constitution of the individual, comprising the ALLELES present at each GENETIC LOCUS.Genome, Mitochondrial: The genetic complement of MITOCHONDRIA as represented in their DNA.Software: Sequential operating programs and data which instruct the functioning of a digital computer.Reproducibility of Results: The statistical reproducibility of measurements (often in a clinical context), including the testing of instrumentation or techniques to obtain reproducible results. The concept includes reproducibility of physiological measurements, which may be used to develop rules to assess probability or prognosis, or response to a stimulus; reproducibility of occurrence of a condition; and reproducibility of experimental results.Genetic Markers: A phenotypically recognizable genetic trait which can be used to identify a genetic locus, a linkage group, or a recombination event.Photic Stimulation: Investigative technique commonly used during ELECTROENCEPHALOGRAPHY in which a series of bright light flashes or visual patterns are used to elicit brain activity.Sequence Alignment: The arrangement of two or more amino acid or base sequences from an organism or organisms in such a way as to align areas of the sequences sharing common properties. The degree of relatedness or homology between the sequences is predicted computationally or statistically based on weights assigned to the elements aligned between the sequences. This in turn can serve as a potential indicator of the genetic relatedness between the organisms.Amino Acid Sequence: The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.Restriction Mapping: Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA.Genetic Predisposition to Disease: A latent susceptibility to disease at the genetic level, which may be activated under certain conditions.RNA, Messenger: RNA sequences that serve as templates for protein synthesis. Bacterial mRNAs are generally primary transcripts in that they do not require post-transcriptional processing. Eukaryotic mRNA is synthesized in the nucleus and must be exported to the cytoplasm for translation. Most eukaryotic mRNAs have a sequence of polyadenylic acid at the 3' end, referred to as the poly(A) tail. The function of this tail is not known for certain, but it may play a role in the export of mature mRNA from the nucleus as well as in helping stabilize some mRNA molecules by retarding their degradation in the cytoplasm.Evolution, Molecular: The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.DNA, Bacterial: Deoxyribonucleic acid that makes up the genetic material of bacteria.Principal Component Analysis: Mathematical procedure that transforms a number of possibly correlated variables into a smaller number of uncorrelated variables called principal components.DNA, Plant: Deoxyribonucleic acid that makes up the genetic material of plants.Protein-Arginine N-Methyltransferases: Enzymes that catalyze the methylation of arginine residues of proteins to yield N-mono- and N,N-dimethylarginine. This enzyme is found in many organs, primarily brain and spleen.Species Specificity: The restriction of a characteristic behavior, anatomical structure or physical system, such as immune response; metabolic response, or gene or gene variant to the members of one species. It refers to that property which differentiates one species from another but it is also used for phylogenetic levels higher or lower than the species.RNA, Untranslated: RNA which does not code for protein but has some enzymatic, structural or regulatory function. Although ribosomal RNA (RNA, RIBOSOMAL) and transfer RNA (RNA, TRANSFER) are also untranslated RNAs they are not included in this scope.Death-Associated Protein Kinases: A family of calcium/calmodulin-dependent PROETIN-SERINE-THREONINE KINASES. They are ubiquitously expressed in adult and embryonic mammalian tissues, and their functions are tightly related to the early stages of eukaryotic programmed cell death.Reverse Transcriptase Polymerase Chain Reaction: A variation of the PCR technique in which cDNA is made from RNA via reverse transcription. The resultant cDNA is then amplified using standard PCR protocols.Gene Expression Regulation, Plant: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in plants.Pattern Recognition, Visual: Mental process to visually perceive a critical number of facts (the pattern), such as characters, shapes, displays, or designs.Colonoscopes: Specially designed endoscopes for visualizing the interior surface of the colon.Genetic Variation: Genotypic differences observed among individuals in a population.Genome, Insect: The genetic complement of an insect (INSECTS) as represented in its DNA.Chromatin Immunoprecipitation: A technique for identifying specific DNA sequences that are bound, in vivo, to proteins of interest. It involves formaldehyde fixation of CHROMATIN to crosslink the DNA-BINDING PROTEINS to the DNA. After shearing the DNA into small fragments, specific DNA-protein complexes are isolated by immunoprecipitation with protein-specific ANTIBODIES. Then, the DNA isolated from the complex can be identified by PCR amplification and sequencing.Blotting, Southern: A method (first developed by E.M. Southern) for detection of DNA that has been electrophoretically separated and immobilized by blotting on nitrocellulose or other type of paper or nylon membrane followed by hybridization with labeled NUCLEIC ACID PROBES.Tumor Suppressor Proteins: Proteins that are normally involved in holding cellular growth in check. Deficiencies or abnormalities in these proteins may lead to unregulated cell growth and tumor development.Genes, Tumor Suppressor: Genes that inhibit expression of the tumorigenic phenotype. They are normally involved in holding cellular growth in check. When tumor suppressor genes are inactivated or lost, a barrier to normal proliferation is removed and unregulated growth is possible.Alu Elements: The Alu sequence family (named for the restriction endonuclease cleavage enzyme Alu I) is the most highly repeated interspersed repeat element in humans (over a million copies). It is derived from the 7SL RNA component of the SIGNAL RECOGNITION PARTICLE and contains an RNA polymerase III promoter. Transposition of this element into coding and regulatory regions of genes is responsible for many heritable diseases.Heterochromatin: The portion of chromosome material that remains condensed and is transcriptionally inactive during INTERPHASE.Transcription Factors: Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.DNA Primers: Short sequences (generally about 10 base pairs) of DNA that are complementary to sequences of messenger RNA and allow reverse transcriptases to start copying the adjacent sequences of mRNA. Primers are used extensively in genetic and molecular biology techniques.Genome Size: The amount of DNA (or RNA) in one copy of a genome.High-Throughput Nucleotide Sequencing: Techniques of nucleotide sequence analysis that increase the range, complexity, sensitivity, and accuracy of results by greatly increasing the scale of operations and thus the number of nucleotides, and the number of copies of each nucleotide sequenced. The sequencing may be done by analysis of the synthesis or ligation products, hybridization to preexisting sequences, etc.Repetitive Sequences, Nucleic Acid: Sequences of DNA or RNA that occur in multiple copies. There are several types: INTERSPERSED REPETITIVE SEQUENCES are copies of transposable elements (DNA TRANSPOSABLE ELEMENTS or RETROELEMENTS) dispersed throughout the genome. TERMINAL REPEAT SEQUENCES flank both ends of another sequence, for example, the long terminal repeats (LTRs) on RETROVIRUSES. Variations may be direct repeats, those occurring in the same direction, or inverted repeats, those opposite to each other in direction. TANDEM REPEAT SEQUENCES are copies which lie adjacent to each other, direct or inverted (INVERTED REPEAT SEQUENCES).Site-Specific DNA-Methyltransferase (Adenine-Specific): An enzyme responsible for producing a species-characteristic methylation pattern on adenine residues in a specific short base sequence in the host cell DNA. The enzyme catalyzes the methylation of DNA adenine in the presence of S-adenosyl-L-methionine to form DNA containing 6-methylaminopurine and S-adenosyl-L-homocysteine. EC 126.96.36.199.Face: The anterior portion of the head that includes the skin, muscles, and structures of the forehead, eyes, nose, mouth, cheeks, and jaw.Spatio-Temporal Analysis: Techniques which study entities using their topological, geometric, or geographic properties and include the dimension of time in the analysis.Cyclin-Dependent Kinase Inhibitor p16: A product of the p16 tumor suppressor gene (GENES, P16). It is also called INK4 or INK4A because it is the prototype member of the INK4 CYCLIN-DEPENDENT KINASE INHIBITORS. This protein is produced from the alpha mRNA transcript of the p16 gene. The other gene product, produced from the alternatively spliced beta transcript, is TUMOR SUPPRESSOR PROTEIN P14ARF. Both p16 gene products have tumor suppressor functions.Cyclin-Dependent Kinase Inhibitor p15: An INK4 cyclin-dependent kinase inhibitor containing four ANKYRIN-LIKE REPEATS. INK4B is often inactivated by deletions, mutations, or hypermethylation in HEMATOLOGIC NEOPLASMS.Temporal Lobe: Lower lateral part of the cerebral hemisphere responsible for auditory, olfactory, and semantic processing. It is located inferior to the lateral fissure and anterior to the OCCIPITAL LOBE.Insulin-Like Growth Factor II: A well-characterized neutral peptide believed to be secreted by the LIVER and to circulate in the BLOOD. It has growth-regulating, insulin-like and mitogenic activities. The growth factor has a major, but not absolute, dependence on SOMATOTROPIN. It is believed to be a major fetal growth factor in contrast to INSULIN-LIKE GROWTH FACTOR I, which is a major growth factor in adults.Arabidopsis: A plant genus of the family BRASSICACEAE that contains ARABIDOPSIS PROTEINS and MADS DOMAIN PROTEINS. The species A. thaliana is used for experiments in classical plant genetics as well as molecular genetic studies in plant physiology, biochemistry, and development.Acetylation: Formation of an acetyl derivative. (Stedman, 25th ed)Image Interpretation, Computer-Assisted: Methods developed to aid in the interpretation of ultrasound, radiographic images, etc., for diagnosis of disease.Visual Perception: The selecting and organizing of visual stimuli based on the individual's past experience.Genome, Archaeal: The genetic complement of an archaeal organism (ARCHAEA) as represented in its DNA.S-Adenosylhomocysteine: 5'-S-(3-Amino-3-carboxypropyl)-5'-thioadenosine. Formed from S-adenosylmethionine after transmethylation reactions.Databases, Genetic: Databases devoted to knowledge about specific genes and gene products.Microsatellite Repeats: A variety of simple repeat sequences that are distributed throughout the GENOME. They are characterized by a short repeat unit of 2-8 basepairs that is repeated up to 100 times. They are also known as short tandem repeats (STRs).DNA-Binding Proteins: Proteins which bind to DNA. The family includes proteins which bind to both double- and single-stranded DNA and also includes specific DNA binding proteins in serum which can be used as markers for malignant diseases.Time Factors: Elements of limited time intervals, contributing to particular results or situations.Nuclear Proteins: Proteins found in the nucleus of a cell. Do not confuse with NUCLEOPROTEINS which are proteins conjugated with nucleic acids, that are not necessarily present in the nucleus.Gene Expression: The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION.Repressor Proteins: Proteins which maintain the transcriptional quiescence of specific GENES or OPERONS. Classical repressor proteins are DNA-binding proteins that are normally bound to the OPERATOR REGION of an operon, or the ENHANCER SEQUENCES of a gene until a signal occurs that causes their release.Genetic Linkage: The co-inheritance of two or more non-allelic GENES due to their being located more or less closely on the same CHROMOSOME.DNA Restriction Enzymes: Enzymes that are part of the restriction-modification systems. They catalyze the endonucleolytic cleavage of DNA sequences which lack the species-specific methylation pattern in the host cell's DNA. Cleavage yields random or specific double-stranded fragments with terminal 5'-phosphates. The function of restriction enzymes is to destroy any foreign DNA that invades the host cell. Most have been studied in bacterial systems, but a few have been found in eukaryotic organisms. They are also used as tools for the systematic dissection and mapping of chromosomes, in the determination of base sequences of DNAs, and have made it possible to splice and recombine genes from one organism into the genome of another. EC 3.21.1.Euchromatin: Chromosome regions that are loosely packaged and more accessible to RNA polymerases than HETEROCHROMATIN. These regions also stain differentially in CHROMOSOME BANDING preparations.Gene Expression Regulation, Developmental: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action during the developmental stages of an organism.DNA, Viral: Deoxyribonucleic acid that makes up the genetic material of viruses.Quantitative Trait Loci: Genetic loci associated with a QUANTITATIVE TRAIT.Transcriptome: The pattern of GENE EXPRESSION at the level of genetic transcription in a specific organism or under specific circumstances in specific cells.Exons: The parts of a transcript of a split GENE remaining after the INTRONS are removed. They are spliced together to become a MESSENGER RNA or other functional RNA.Chromosomes, Human, X: The human female sex chromosome, being the differential sex chromosome carried by half the male gametes and all female gametes in humans.Case-Control Studies: Studies which start with the identification of persons with a disease of interest and a control (comparison, referent) group without the disease. The relationship of an attribute to the disease is examined by comparing diseased and non-diseased persons with regard to the frequency or levels of the attribute in each group.Binding Sites: The parts of a macromolecule that directly participate in its specific combination with another molecule.Embryonic Stem Cells: Cells derived from the BLASTOCYST INNER CELL MASS which forms before implantation in the uterine wall. They retain the ability to divide, proliferate and provide progenitor cells that can differentiate into specialized cells.Genome, Protozoan: The complete genetic complement contained in a set of CHROMOSOMES in a protozoan.Occipital Lobe: Posterior portion of the CEREBRAL HEMISPHERES responsible for processing visual sensory information. It is located posterior to the parieto-occipital sulcus and extends to the preoccipital notch.Genes, Plant: The functional hereditary units of PLANTS.Prader-Willi Syndrome: An autosomal dominant disorder caused by deletion of the proximal long arm of the paternal chromosome 15 (15q11-q13) or by inheritance of both of the pair of chromosomes 15 from the mother (UNIPARENTAL DISOMY) which are imprinted (GENETIC IMPRINTING) and hence silenced. Clinical manifestations include MENTAL RETARDATION; MUSCULAR HYPOTONIA; HYPERPHAGIA; OBESITY; short stature; HYPOGONADISM; STRABISMUS; and HYPERSOMNOLENCE. (Menkes, Textbook of Child Neurology, 5th ed, p229)Neuroimaging: Non-invasive methods of visualizing the CENTRAL NERVOUS SYSTEM, especially the brain, by various imaging modalities.DNA Transposable Elements: Discrete segments of DNA which can excise and reintegrate to another site in the genome. Most are inactive, i.e., have not been found to exist outside the integrated state. DNA transposable elements include bacterial IS (insertion sequence) elements, Tn elements, the maize controlling elements Ac and Ds, Drosophila P, gypsy, and pogo elements, the human Tigger elements and the Tc and mariner elements which are found throughout the animal kingdom.Genes, Neoplasm: Genes whose abnormal expression, or MUTATION are associated with the development, growth, or progression of NEOPLASMS.Sensitivity and Specificity: Binary classification measures to assess test results. Sensitivity or recall rate is the proportion of true positives. Specificity is the probability of correctly determining the absence of a condition. (From Last, Dictionary of Epidemiology, 2d ed)Visual Cortex: Area of the OCCIPITAL LOBE concerned with the processing of visual information relayed via VISUAL PATHWAYS.Deoxyribonucleases, Type II Site-Specific: Enzyme systems containing a single subunit and requiring only magnesium for endonucleolytic activity. The corresponding modification methylases are separate enzymes. The systems recognize specific short DNA sequences and cleave either within, or at a short specific distance from, the recognition sequence to give specific double-stranded fragments with terminal 5'-phosphates. Enzymes from different microorganisms with the same specificity are called isoschizomers. EC 188.8.131.52.Genes: A category of nucleic acid sequences that function as units of heredity and which code for the basic instructions for the development, reproduction, and maintenance of organisms.Base Composition: The relative amounts of the PURINES and PYRIMIDINES in a nucleic acid.Oxygen: An element with atomic symbol O, atomic number 8, and atomic weight [15.99903; 15.99977]. It is the most abundant element on earth and essential for respiration.Angelman Syndrome: A syndrome characterized by multiple abnormalities, MENTAL RETARDATION, and movement disorders. Present usually are skull and other abnormalities, frequent infantile spasms (SPASMS, INFANTILE); easily provoked and prolonged paroxysms of laughter (hence "happy"); jerky puppetlike movements (hence "puppet"); continuous tongue protrusion; motor retardation; ATAXIA; MUSCLE HYPOTONIA; and a peculiar facies. It is associated with maternal deletions of chromosome 15q11-13 and other genetic abnormalities. (From Am J Med Genet 1998 Dec 4;80(4):385-90; Hum Mol Genet 1999 Jan;8(1):129-35)Neoplasms: New abnormal growth of tissue. Malignant neoplasms show a greater degree of anaplasia and have the properties of invasion and metastasis, compared to benign neoplasms.Embryo, Mammalian: The entity of a developing mammal (MAMMALS), generally from the cleavage of a ZYGOTE to the end of embryonic differentiation of basic structures. For the human embryo, this represents the first two months of intrauterine development preceding the stages of the FETUS.Tumor Markers, Biological: Molecular products metabolized and secreted by neoplastic tissue and characterized biochemically in cells or body fluids. They are indicators of tumor stage and grade as well as useful for monitoring responses to treatment and predicting recurrence. Many chemical groups are represented including hormones, antigens, amino and nucleic acids, enzymes, polyamines, and specific cell membrane proteins and lipids.Asparagus Plant: A plant genus in the family LILIACEAE (sometimes placed in Asparagaceae) that contains ECDYSTEROIDS and is an ingredient of Siotone. The shoots are used as a vegetable and the roots are used in FOLK MEDICINE.Linkage Disequilibrium: Nonrandom association of linked genes. This is the tendency of the alleles of two separate but already linked loci to be found together more frequently than would be expected by chance alone.Inheritance Patterns: The different ways GENES and their ALLELES interact during the transmission of genetic traits that effect the outcome of GENE EXPRESSION.Protein Binding: The process in which substances, either endogenous or exogenous, bind to proteins, peptides, enzymes, protein precursors, or allied compounds. Specific protein-binding measures are often used as assays in diagnostic assessments.Cloning, Molecular: The insertion of recombinant DNA molecules from prokaryotic and/or eukaryotic sources into a replicating vehicle, such as a plasmid or virus vector, and the introduction of the resultant hybrid molecules into recipient cells without altering the viability of those cells.Cytidine: A pyrimidine nucleoside that is composed of the base CYTOSINE linked to the five-carbon sugar D-RIBOSE.Multivariate Analysis: A set of techniques used when variation in several variables has to be studied simultaneously. In statistics, multivariate analysis is interpreted as any analytic method that allows simultaneous study of two or more dependent variables.Bacterial Typing Techniques: Procedures for identifying types and strains of bacteria. The most frequently employed typing systems are BACTERIOPHAGE TYPING and SEROTYPING as well as bacteriocin typing and biotyping.Transcription Initiation Site: The first nucleotide of a transcribed DNA sequence where RNA polymerase (DNA-DIRECTED RNA POLYMERASE) begins synthesizing the RNA transcript.Embryonic Development: Morphological and physiological development of EMBRYOS.Polymorphism, Restriction Fragment Length: Variation occurring within a species in the presence or length of DNA fragment generated by a specific endonuclease at a specific site in the genome. Such variations are generated by mutations that create or abolish recognition sites for these enzymes or change the length of the fragment.Colorectal Neoplasms: Tumors or cancer of the COLON or the RECTUM or both. Risk factors for colorectal cancer include chronic ULCERATIVE COLITIS; FAMILIAL POLYPOSIS COLI; exposure to ASBESTOS; and irradiation of the CERVIX UTERI.Breast Neoplasms: Tumors or cancer of the human BREAST.Spermatozoa: Mature male germ cells derived from SPERMATIDS. As spermatids move toward the lumen of the SEMINIFEROUS TUBULES, they undergo extensive structural changes including the loss of cytoplasm, condensation of CHROMATIN into the SPERM HEAD, formation of the ACROSOME cap, the SPERM MIDPIECE and the SPERM TAIL that provides motility.Recognition (Psychology): The knowledge or perception that someone or something present has been previously encountered.Plasmids: Extrachromosomal, usually CIRCULAR DNA molecules that are self-replicating and transferable from one organism to another. They are found in a variety of bacterial, archaeal, fungal, algal, and plant species. They are used in GENETIC ENGINEERING as CLONING VECTORS.Bacterial Proteins: Proteins found in any species of bacterium.Glutathione S-Transferase pi: A glutathione transferase that catalyzes the conjugation of electrophilic substrates to GLUTATHIONE. This enzyme has been shown to provide cellular protection against redox-mediated damage by FREE RADICALS.Oryza sativa: Annual cereal grass of the family POACEAE and its edible starchy grain, rice, which is the staple food of roughly one-half of the world's population.Germ Cells: The reproductive cells in multicellular organisms at various stages during GAMETOGENESIS.Beckwith-Wiedemann Syndrome: A syndrome of multiple defects characterized primarily by umbilical hernia (HERNIA, UMBILICAL); MACROGLOSSIA; and GIGANTISM; and secondarily by visceromegaly; HYPOGLYCEMIA; and ear abnormalities.Nucleic Acid Hybridization: Widely used technique which exploits the ability of complementary sequences in single-stranded DNAs or RNAs to pair with each other to form a double helix. Hybridization can take place between two complimentary DNA sequences, between a single-stranded DNA and a complementary RNA, or between two RNA sequences. The technique is used to detect and isolate specific sequences, measure homology, or define other characteristics of one or both strands. (Kendrew, Encyclopedia of Molecular Biology, 1994, p503)Neoplasm Proteins: Proteins whose abnormal expression (gain or loss) are associated with the development, growth, or progression of NEOPLASMS. Some neoplasm proteins are tumor antigens (ANTIGENS, NEOPLASM), i.e. they induce an immune reaction to their tumor. Many neoplasm proteins have been characterized and are used as tumor markers (BIOMARKERS, TUMOR) when they are detectable in cells and body fluids as monitors for the presence or growth of tumors. Abnormal expression of ONCOGENE PROTEINS is involved in neoplastic transformation, whereas the loss of expression of TUMOR SUPPRESSOR PROTEINS is involved with the loss of growth control and progression of the neoplasm.Tumor Cells, Cultured: Cells grown in vitro from neoplastic tissue. If they can be established as a TUMOR CELL LINE, they can be propagated in cell culture indefinitely.Pregnancy: The status during which female mammals carry their developing young (EMBRYOS or FETUSES) in utero before birth, beginning from FERTILIZATION to BIRTH.Lod Score: The total relative probability, expressed on a logarithmic scale, that a linkage relationship exists among selected loci. Lod is an acronym for "logarithmic odds."Hydroxamic Acids: A class of weak acids with the general formula R-CONHOH.Polycomb-Group Proteins: A family of proteins that play a role in CHROMATIN REMODELING. They are best known for silencing HOX GENES and the regulation of EPIGENETIC PROCESSES.Molecular Sequence Annotation: The addition of descriptive information about the function or structure of a molecular sequence to its MOLECULAR SEQUENCE DATA record.DNA Repair Enzymes: Enzymes that are involved in the reconstruction of a continuous two-stranded DNA molecule without mismatch from a molecule, which contained damaged regions.Proteins: Linear POLYPEPTIDES that are synthesized on RIBOSOMES and may be further modified, crosslinked, cleaved, or assembled into complex proteins with several subunits. The specific sequence of AMINO ACIDS determines the shape the polypeptide will take, during PROTEIN FOLDING, and the function of the protein.Pedigree: The record of descent or ancestry, particularly of a particular condition or trait, indicating individual family members, their relationships, and their status with respect to the trait or condition.Gene Frequency: The proportion of one particular in the total of all ALLELES for one genetic locus in a breeding POPULATION.Multigene Family: A set of genes descended by duplication and variation from some ancestral gene. Such genes may be clustered together on the same chromosome or dispersed on different chromosomes. Examples of multigene families include those that encode the hemoglobins, immunoglobulins, histocompatibility antigens, actins, tubulins, keratins, collagens, heat shock proteins, salivary glue proteins, chorion proteins, cuticle proteins, yolk proteins, and phaseolins, as well as histones, ribosomal RNA, and transfer RNA genes. The latter three are examples of reiterated genes, where hundreds of identical genes are present in a tandem array. (King & Stanfield, A Dictionary of Genetics, 4th ed)Chromosomes: In a prokaryotic cell or in the nucleus of a eukaryotic cell, a structure consisting of or containing DNA which carries the genetic information essential to the cell. (From Singleton & Sainsbury, Dictionary of Microbiology and Molecular Biology, 2d ed)DNA Fingerprinting: A technique for identifying individuals of a species that is based on the uniqueness of their DNA sequence. Uniqueness is determined by identifying which combination of allelic variations occur in the individual at a statistically relevant number of different loci. In forensic studies, RESTRICTION FRAGMENT LENGTH POLYMORPHISM of multiple, highly polymorphic VNTR LOCI or MICROSATELLITE REPEAT loci are analyzed. The number of loci used for the profile depends on the ALLELE FREQUENCY in the population.DNA, Intergenic: Any of the DNA in between gene-coding DNA, including untranslated regions, 5' and 3' flanking regions, INTRONS, non-functional pseudogenes, and non-functional repetitive sequences. This DNA may or may not encode regulatory functions.Haplotypes: The genetic constitution of individuals with respect to one member of a pair of allelic genes, or sets of genes that are closely linked and tend to be inherited together such as those of the MAJOR HISTOCOMPATIBILITY COMPLEX.Organ Specificity: Characteristic restricted to a particular organ of the body, such as a cell type, metabolic response or expression of a particular protein or antigen.Dosage Compensation, Genetic: Genetic mechanisms that allow GENES to be expressed at a similar level irrespective of their GENE DOSAGE. This term is usually used in discussing genes that lie on the SEX CHROMOSOMES. Because the sex chromosomes are only partially homologous, there is a different copy number, i.e., dosage, of these genes in males vs. females. In DROSOPHILA, dosage compensation is accomplished by hypertranscription of genes located on the X CHROMOSOME. In mammals, dosage compensation of X chromosome genes is accomplished by random X CHROMOSOME INACTIVATION of one of the two X chromosomes in the female.Methyl-CpG-Binding Protein 2: A DNA-binding protein that interacts with methylated CPG ISLANDS. It plays a role in repressing GENETIC TRANSCRIPTION and is frequently mutated in RETT SYNDROME.Genomic Instability: An increased tendency of the GENOME to acquire MUTATIONS when various processes involved in maintaining and replicating the genome are dysfunctional.O(6)-Methylguanine-DNA Methyltransferase: An enzyme that transfers methyl groups from O(6)-methylguanine, and other methylated moieties of DNA, to a cysteine residue in itself, thus repairing alkylated DNA in a single-step reaction. EC 184.108.40.206.tRNA Methyltransferases: Enzymes that catalyze the S-adenosyl-L-methionine-dependent methylation of ribonucleotide bases within a transfer RNA molecule. EC 2.1.1.Feeding Behavior: Behavioral responses or sequences associated with eating including modes of feeding, rhythmic patterns of eating, and time intervals.Genome, Chloroplast: The genetic complement of CHLOROPLASTS as represented in their DNA.Arabidopsis Proteins: Proteins that originate from plants species belonging to the genus ARABIDOPSIS. The most intensely studied species of Arabidopsis, Arabidopsis thaliana, is commonly used in laboratory experiments.Arsenic: A shiny gray element with atomic symbol As, atomic number 33, and atomic weight 75. It occurs throughout the universe, mostly in the form of metallic arsenides. Most forms are toxic. According to the Fourth Annual Report on Carcinogens (NTP 85-002, 1985), arsenic and certain arsenic compounds have been listed as known carcinogens. (From Merck Index, 11th ed)Conserved Sequence: A sequence of amino acids in a polypeptide or of nucleotides in DNA or RNA that is similar across multiple species. A known set of conserved sequences is represented by a CONSENSUS SEQUENCE. AMINO ACID MOTIFS are often composed of conserved sequences.
"A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promoters". Proceedings ... Bird A (January 2002). "DNA methylation patterns and epigenetic memory". Genes & Development. 16 (1): 6-21. doi:10.1101/gad. ... HIV has an RNA genome that is reverse transcribed into DNA. The resulting DNA can be merged with the DNA genome of the host ... The effects of histone methylation may also work to inhibit the action of transcription. In vertebrates, the majority of gene ...
"A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promoters". Proceedings ... "DNA methylation patterns and epigenetic memory". Genes & Development. 16 (1): 6-21. doi:10.1101/gad.947102. PMID 11782440.. ... HIV has an RNA genome that is reverse transcribed into DNA. The resulting DNA can be merged with the DNA genome of the host ... Genome. *Crick's central dogma, in which the product of transcription, mRNA, is translated to form polypeptides, and where it ...
Saxonov S, Berg P, Brutlag DL (2006). "A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two ... Bird A (2002). "DNA methylation patterns and epigenetic memory". Genes Dev. 16 (1): 6-21. doi:10.1101/gad.947102. PMID 11782440 ... and/or DNA methylation. The gene expression patterns that define cell identity are inherited through cell division. This ... The eukaryotic genome is organized into a compact chromatin structure that allows only regulated access to DNA. The chromatin ...
Saxonov S, Berg P, Brutlag DL (2006). "A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two ... Bird A (2002). "DNA methylation patterns and epigenetic memory". Genes Dev. 16 (1): 6-21. doi:10.1101/gad.947102. PMID 11782440 ... "Widespread plasticity in CTCF occupancy linked to DNA methylation". Genome Research. 22 (9): 1680-8. doi:10.1101/gr.136101.111 ... The most relevant study on limb evolution shows that the TAD at the 5' of the HoxD gene cluster in tetrapod genomes drives its ...
Regulation of gene expression
Saxonov S, Berg P, Brutlag DL (2006). "A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two ... Analysis of the pattern of methylation in a given region of DNA (which can be a promoter) can be achieved through a method ... Schwanekamp JA, Sartor MA, Karyala S, Halbleib D, Medvedovic M, Tomlinson CR (2006). "Genome-wide analyses show that nuclear ... "DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines". Genome Biology. 12 (1): ...
Saxonov S, Berg P, Brutlag DL (2006). "A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two ... Bird A (2002). "DNA methylation patterns and epigenetic memory". Genes Dev. 16 (1): 6-21. doi:10.1101/gad.947102. PMID 11782440 ... 2008). "Annotating genomes with massive-scale RNA sequencing". Genome Biol. 9 (12): R175. doi:10.1186/gb-2008-9-12-r175. PMC ... DNA methylation is a widespread mechanism for epigenetic influence on gene expression and is seen in bacteria and eukaryotes ...
Whole genome bisulfite sequencing, also known as BS-Seq, which is a high-throughput genome-wide analysis of DNA methylation. It ... "A six months exercise intervention influences the genome-wide DNA methylation pattern in human adipose tissue". PLOS Genetics. ... Saxonov, Serge; Berg, Paul; Brutlag, Douglas L. (2006-01-31). "A genome-wide analysis of CpG dinucleotides in the human genome ... "Genome-Wide Evolutionary Analysis of Eukaryotic DNA Methylation". Science. 328 (5980): 916-919. doi:10.1126/science.1186366. ...
Methylated DNA immunoprecipitation
September 2006). "Genome-wide high-resolution mapping and functional analysis of DNA methylation in arabidopsis". Cell. 126 (6 ... patterns vary from cell-type to cell-type. DNA methylation, referring to the reversible methylation of the 5 position of ... Pomraning KR, Smith KM, Freitag M (March 2009). "Genome-wide high throughput analysis of DNA methylation in eukaryotes". ... "Gene-Set Analysis is Severely Biased When Applied to Genome-wide Methylation Data". Bioinformatics. 29 (15): 1851-7. doi: ...
Illumina Methylation Assay
The method looks at ~2 CpG sites per CpG island, providing genome-wide coverage of methylation patterns Disadvantages Not every ... in the diploid human genome. Analysis of methylation data The scanned microarray images of methylation data are further ... DNA methylation Collection in Nature Reviews DNA/Methylation Analysis Protocols Illumina, Infinium Methylation OMICtools: an ... A large scale measurement of DNA methylation patterns from a wide selection of genes may enable us to understand better the ...
Differentially methylated regions
In a study published in 2013, Delgado-Calle and colleagues compared genome-wide methylation patterns in women with osteoporosis ... "Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human ... "Genome-wide DNA methylation patterns in CD4+ T cells from patients with systemic lupus erythematosus". Epigenetics. 6 (5): 593- ... is a quantitative approach to quantify methylation difference and identify DMRs from genome-wide methylation profiles by ...
Whole genome bisulfite sequencing, also known as BS-Seq, which is a high-throughput genome-wide analysis of DNA methylation. It ... DNA methylation marks. DNA methylation marks - genomic regions with specific methylation pattern in a specific biological ... Zemach A, McDaniel IE, Silva P, Zilberman D (May 2010). "Genome-wide evolutionary analysis of eukaryotic DNA methylation". ... "A six months exercise intervention influences the genome-wide DNA methylation pattern in human adipose tissue". PLoS Genetics. ...
DNA methylation in cancer
Saxonov S, Berg P, Brutlag DL (2006). "A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two ... Bird A (2002). "DNA methylation patterns and epigenetic memory". Genes Dev. 16 (1): 6-21. doi:10.1101/gad.947102. PMID 11782440 ... Li Y, Zhang Y, Li S, Lu J, Chen J, Wang Y, Li Y, Xu J, Li X (2015). "Genome-wide DNA methylome analysis reveals epigenetically ... Beggs AD, Jones A, El-Bahrawy M, El-Bahwary M, Abulafi M, Hodgson SV, Tomlinson IP (2013). "Whole-genome methylation analysis ...
Gene set enrichment analysis
"Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles". Proceedings of the ... Researchers ranked genes for their correlation between methylation patterns and each of the phenotypes. They then used GSEA to ... applying gene set enrichment analysis to SNP data from genome-wide association studies". Bioinformatics. 24 (23): 2784-2785. ... Genome-wide association studies are comparisons between healthy and disease genotypes to try to find SNPs that are ...
Schwanekamp JA, Sartor MA, Karyala S, Halbleib D, Medvedovic M, Tomlinson CR (2006). "Genome-wide analyses show that nuclear ... analysis of DNA methylation patterns of the putative promoter region". Oncogene. 17 (24): 3169-76. doi:10.1038/sj.onc.1202248. ... MicroRNAs (miRNAs) appear to regulate the expression of more than 60% of protein coding genes of the human genome. If an miRNA ... Jackson DA, Pombo A, Iborra F (2000). "The balance sheet for transcription: an analysis of nuclear RNA metabolism in mammalian ...
"A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promoters". Proc Natl ... Bird A (2002). "DNA methylation patterns and epigenetic memory". Genes Dev. 16 (1): 6-21. doi:10.1101/gad.947102. PMID 11782440 ... "A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promoters". Proc. Natl. ... "Whole-genome methylation analysis of benign and malignant colorectal tumours". J. Pathol. 229 (5): 697-704. doi:10.1002/path. ...
"A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promoters". Proc. Natl. ... Bird A (2002). "DNA methylation patterns and epigenetic memory". Genes Dev. 16 (1): 6-21. doi:10.1101/gad.947102. PMID 11782440 ... Liu, Bingchuan; Chen, Jiajia; Shen, Bairong (2011). "Genome-wide analysis of the transcription factor binding preference of ... see DNA methylation in cancer). DNA methylation causing silencing in cancer typically occurs at multiple CpG sites in the CpG ...
Gene and SNP sets found by genome-wide association analysis of epigenetic age acceleration exhibit significant overlap with ... Changes to DNA methylation patterns have great potential for age estimation and biomarker search in domestic and wild animals. ... Genome-wide association studies of cerebellar age acceleration have identified several SNPs at a genomewide significance level ... "Genome-wide methylation profiles reveal quantitative views of human aging rates". Mol Cell. 49: 359-367. doi:10.1016/j.molcel. ...
Saxonov S, Berg P, Brutlag DL (2006). "A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two ... Bird A (2002). "DNA methylation patterns and epigenetic memory". Genes Dev. 16 (1): 6-21. doi:10.1101/gad.947102. PMID 11782440 ... Saxonov S, Berg P, Brutlag DL (2006). "A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two ... Beggs AD, Jones A, El-Bahrawy M, El-Bahwary M, Abulafi M, Hodgson SV, Tomlinson IP (2013). "Whole-genome methylation analysis ...
"Gene-Set Analysis is Severely Biased When Applied to Genome-wide Methylation Data". Bioinformatics. 29 (15): 1851-7. doi: ... November 2005). "Quantitative high-throughput analysis of DNA methylation patterns by base-specific cleavage and mass ... Other non-sequencing strategies are also employed to interrogate the methylation at specific loci or at a genome-wide level. ... extension of the technologies available to analyze bisulfite-treated DNA to allow for genome-wide analysis of methylation. ...
MethDB Contains information on 19,905 DNA methylation content data and 5,382 methylation patterns for 48 species, 1,511 ... Various experimental techniques have been developed for genome-wide mapping of epigenetic information, the most widely used ... associated gene methylation and cancer information from text mining methPrimerDB: the DNA methylation analysis PCR primer ... MethPrimerDB Contains 259 primer sets from human, mouse and rat for DNA methylation analysis. The Histone Database Contains 254 ...
Contribution of epigenetic modifications to evolution
A comparative analysis of CpG methylation patterns between humans and primates found that there were more than 800 genes that ... Heritable genome-wide variation of gene expression and promoter methylation between wild and domesticated chickens. BMC ... fragment-length polymorphism markers that were methylation-sensitive were used to test for methylation on a genome-wide scale. ... allowing for methylation states to be passed to other orthologous genes in a genome. DNA methylation can be reversed via the ...
Meyer KD, Saletore Y, Zumbo P, Elemento O, Mason CE, Jaffrey SR (June 2012). "Comprehensive analysis of mRNA methylation ... "Evaluating genome-wide association study-identified breast cancer risk variants in African-American women". PLoS One. 8 (4): ... A >90% reduction of m6A levels in mature plants leads to dramatically altered growth patterns and floral homeotic abnormalities ... Inhibition of m6A methylation via pharmacological inhibition of cellular methylations or more specifically by siRNA-mediated ...
"A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promoters". Proceedings ... "DNA methylation patterns and epigenetic memory". Genes & Development. 16 (1): 6-21. doi:10.1101/gad.947102. PMID 11782440.. ... "Genome-wide analysis of the transcription factor binding preference of human bi-directional promoters and functional annotation ... Promoters of genes associated with diabetes by Genome-wide association studies (GWAS) show specific DNA patterns for each ...
Using genome-wide association studies, his team identified the first genetic markers (SNPs) that exhibit genome-wide ... was unexpected because cell types differ in terms of the their DNA methylation patterns and age related DNA methylation changes ... "An epigenetic clock analysis of race/ethnicity, sex, and coronary heart disease". Genome Biol. 17 (1): 171. doi:10.1186/s13059- ... Horvath, S (2013). "DNA methylation age of human tissues and cell types". Genome Biology. 14: R115. doi:10.1186/gb-2013-14-10- ...
Single cell sequencing
"Genome-wide evolutionary analysis of eukaryotic DNA methylation". Science. 328 (5980): 916-9. Bibcode:2010Sci...328..916Z. doi: ... patterns of gene expression can be identified through gene clustering analyses. This can uncover the existence of rare cell ... Single-cell genome (DNA) sequencing. Single-cell DNA genome sequencing involves isolating a single cell, amplifying the ... Comparing MDA and MALBAC, MDA results in better genome coverage, but MALBAC provides more even coverage across the genome. MDA ...
Epigenome-wide association study (EWAS)
... is an examination of a genome-wide set of quantifiable epigenetic marks, such as DNA methylation, in different individuals to ... "DNA Methylation Array Analysis Identifies Profiles of Blood-Derived DNA Methylation Associated With Bladder Cancer". Journal of ... DNA methylation (DNAm) patterns change over time, and vary between developmental stage and tissue type. The main type of DNAm ... Another method of analysis is using unsupervised clustering to create classes of CpG sites based on similarity of methylation ...
Genome-wide analysis of alternative splicing is a challenging task. Typically, alternatively spliced transcripts have been ... expression of two of these abnormally spliced mRNAs in mammalian cells caused changes in the DNA methylation patterns in those ... Deep sequencing technologies have been used to conduct genome-wide analyses of mRNAs - unprocessed and processed - thus ... 2000). "Estimate of human gene number provided by genome-wide analysis using Tetraodon nigroviridis DNA sequence". Nature ...
"Genome-wide transcriptome mapping analysis identifies organ-specific gene expression patterns along human chromosomes". ... Regev A, Lamb MJ, Jablonka E (July 1998). "The role of DNA methylation in invertebrates: developmental regulation or genome ... July 1998). "A genome-wide transcriptional analysis of the mitotic cell cycle". Mol. Cell. 2 (1): 65-73. doi:10.1016/S1097-2765 ... September 2007). "Domain-wide regulation of gene expression in the human genome". Genome Res. 17 (9): 1286-95. doi:10.1101/gr. ...
Regulation of transcription in cancer
"A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promoters". Proc. Natl. ... Bird A (2002). "DNA methylation patterns and epigenetic memory". Genes Dev. 16 (1): 6-21. doi:10.1101/gad.947102. PMID 11782440 ... Beggs AD, Jones A, El-Bahrawy M, El-Bahwary M, Abulafi M, Hodgson SV, Tomlinson IP (2013). "Whole-genome methylation analysis ... "Genome-wide analysis of gene expression in neuroblastomas detected by mass screening". Cancer Lett. 225 (1): 111-20. doi: ...
Next-generation sequencing is well suited in complementing bisulfite sequencing in genome-wide methylation analysis. While this ... DNA methylation patterns vary greatly between species and even within the same organism. The usage of methylation among animals ... For example, in mouse primordial germ cells, a genome wide de-methylation even occurs; by implantation stage, methylation ... Laird PW (March 2010). "Principles and challenges of genomewide DNA methylation analysis". Nature Reviews. Genetics. 11 (3): ...
Genome-Wide Analysis of DNA Methylation Patterns by High-Throughput Sequencing | SpringerLink
DNA methylation is the paradigm epigenetic modification that is associated with transcriptional repression.... ... Baubec T., Akalin A. (2016) Genome-Wide Analysis of DNA Methylation Patterns by High-Throughput Sequencing. In: Aransay A., ... a comprehensive R package for the analysis of genome-wide DNA methylation profiles. Genome Biol 13:R87. doi: 10.1186/gb-2012-13 ... Zemach A, McDaniel IE, Silva P, Zilberman D (2010) Genome-wide evolutionary analysis of eukaryotic DNA methylation. Science 328 ...
Genome-Wide Analysis of DNA Methylation and Gene Expression Changes in Two Arabidopsis Ecotypes and Their Reciprocal Hybrids |...
Methylation Patterns of Ler and C24 Parents and Their Reciprocal Hybrids. Next, we analyzed the methylation patterns of Ler and ... 2007). Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and ... 2006). Genome-wide high-resolution mapping and functional analysis of DNA methylation in Arabidopsis. Cell 126: 1189-1201. ... Genome-Wide Analysis of DNA Methylation and Gene Expression Changes in Two Arabidopsis Ecotypes and Their Reciprocal Hybrids. ...
Frontiers | The Profiling of DNA Methylation and Its Regulation on Divergent Tenderness in Angus Beef Cattle | Genetics
We characterized the methylation profiles related to beef tenderness and explored methylation distributions on the whole genome ... Importantly, we annotated these DMRs on the bovine genome and explored bio-pathways of underlying genes and methylation ... Importantly, we have annotated these DMRs on bovine genome and explored bio-pathways of underlying genes and methylation ... We characterized the methylation profiles related to beef tenderness and explored DNA methylation distributions on the whole ...
Human Skeletal Muscle Possesses an Epigenetic Memory of Hypertrophy | Scientific Reports
... and gene expression analysis after muscle hypertrophy (loading), return of muscle mass to baseline (unloading), followed by ... indicating a memory of these genes methylation signatures following earlier hypertrophy. Further, UBR5, RPL35a, HEG1, PLA2G16, ... later hypertrophy (reloading). We discovered increased frequency of hypomethylation across the genome after reloading (18,816 ... We report, for the first time in humans, genome-wide DNA methylation (850,000 CpGs) ...
Johanna Klughammer: "Reference genome independent DNA methylation analysis. Mapping genome-wide DNA methylation patterns across ... Whole genome comparison for all bird species with other vertebrate species revealed several distinct macroevolution patterns of ... We proposed to utilize full genome data in phylogenetic analyses, which have been confirmed very successful and have produced a ... Toni Gossmann: The great tit genome and its implications for genome evolution. * Date: Mar 3, 2016 ...
Biology | Free Full-Text | Myogenic Differential Methylation: Diverse Associations with Chromatin Structure | HTML
DMRs co-localized with a variety of chromatin structures, as deduced from ENCODE whole-genome profiles. Myogenic ... For representative genes, we illustrate relationships between DNA methylation, the local chromatin state, DNaseI ... Sati, S.; Ghosh, S.; Jain, V.; Scaria, V.; Sengupta, S. Genome-wide analysis reveals distinct patterns of epigenetic features ... Providing in-depth analyses of the epigenetics of a given gene region from genome-wide profiles of DNA methylation, histone ...
Frontiers | Is DNA Methylation a Ray of Sunshine in Predicting Meningioma Prognosis? | Oncology
The DNA methylation-based meningioma classification published in 2017 used DNA copy number analysis, mutation profiling, and ... Among the mutant genes described above, some have been associated with differential DNA methylation. Herein, we searched for ... Among the mutant genes described above, some have been associated with differential DNA methylation. Herein, we searched for ... and RNA sequencing to distinguish six clinically relevant methylation classes, which contributed to a better prediction of ...
Studies of genome-wide patterns of gene expression and methylation in osteosarcoma
Epigenetic regulation of miRNA in osteosarcoma; an integrated analysis of genome-wide miRNA and DNA methylation changes. ... Studies of genome-wide patterns of gene expression and methylation in osteosarcoma. Namløs, Heidi Maria ... Global gene expression profiling of human osteosarcomas reveals metastasis-associated chemokine pattern. Sarcoma 2012: 639038. ...
DNA methylation analysis of the temporal artery microenvironment in giant cell arteritis | Annals of the Rheumatic Diseases
Genome-wide DNA methylation status was evaluated using the Illumina Infinium HumanMethylation450 BeadChip Array. Differentially ... Objective To investigate the inflammatory response in giant cell arteritis (GCA) by characterising the DNA methylation pattern ... DNA methylation analysis of the temporal artery microenvironment in giant cell arteritis ... DNA methylation analysis of the temporal artery microenvironment in giant cell arteritis ...
Discovery of Novel Methylation Biomarkers in Cervical Carcinoma by Global Demethylation and Microarray Analysis | Cancer...
Eisen MB, Spellman PT, Brown PO, Botstein D. Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad ... The present study was undertaken to find such genes using a genome-wide examination of the methylation pattern of cervical ... Detection of CpG Methylation. Genes selected for methylation analysis were evaluated using methylation specific PCR (MSP), ... Methylation Analysis of Candidate Genes in Cell Lines. The methylation of CpG islands associated with the majority of candidate ...
Genome-wide analysis of differential transcriptional and epigenetic variability across human immune cell types | Genome Biology...
Neutrophil-specific DNA methylation hypervariable sites are enriched at dynamic chromatin regions and active enhancers. Our ... We apply a novel analytical approach to measure and compare transcriptional and epigenetic variability genome-wide across CD14+ ... Genome-wide patterns of differential DNA methylation variability across immune cell types. Following the analyses of ... Genome-wide signatures of differential DNA methylation in pediatric acute lymphoblastic leukemia. Genome Biol. 2013;14:r105. ...
Listgarten J[au] - PubMed - NCBI
Patterns of methylation heritability in a genome-wide analysis of four brain regions. ... A genome-to-genome analysis of associations between human genetic variation, HIV-1 sequence diversity, and viral control. ... FaST linear mixed models for genome-wide association studies.. Lippert C, Listgarten J, Liu Y, Kadie CM, Davidson RI, Heckerman ... Improved linear mixed models for genome-wide association studies.. Listgarten J, Lippert C, Kadie CM, Davidson RI, Eskin E, ...
Genome-Wide Identification of a Methylation Gene Panel as a Prognostic Biomarker in Nasopharyngeal Carcinoma | Molecular Cancer...
Genome-wide methylation analysis demonstrated that NPC tissues had distinct DNA methylation patterns compared with NCNBT. Among ... Genome-Wide Identification of a Methylation Gene Panel as a Prognostic Biomarker in Nasopharyngeal Carcinoma. Wei Jiang, Na Liu ... Genome-Wide Identification of a Methylation Gene Panel as a Prognostic Biomarker in Nasopharyngeal Carcinoma ... Genome-Wide Identification of a Methylation Gene Panel as a Prognostic Biomarker in Nasopharyngeal Carcinoma ...
Genome-Wide Identification of a Methylation Gene Panel as a Prognostic Biomarker in Nasopharyngeal Carcinoma | Molecular Cancer...
Genome-wide methylation analysis demonstrated that NPC tissues had distinct DNA methylation patterns compared with NCNBT. Among ... Genome-wide screen of promoter methylation identifies novel markers in melanoma. Genome Res 2009;19:1462-70. ... We employed genome-wide methylation microarray to identify a hypermethylated methylation gene panel in a discovery set of 24 ... Genome-wide methylation profiling. We used an Infinium Human Methylation 450K BeadChip (Illumina) according to the ...
Isogenic mice exhibit sexually-dimorphic DNA methylation patterns across multiple tissues | BMC Genomics | Full Text
DNA methylation patterns varied significantly from tissue to tissue, as expected, but they also varied between the sexes, with ... To address this deficit we studied DNA methylation patterns across multiple reduced representation bisulphite sequencing ... Cytosine methylation is a stable epigenetic modification of DNA that plays an important role in both normal physiology and ... methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles. Genome Biol. 2012;13(10):R87. ...
Molecular characteristics of early-stage female germ cells revealed by RNA sequencing of low-input cells and analysis of genome...
Genome-wide DNA methylation patterns during female germline development and methylome comparison of fresh and cultured FGSCs. ( ... Analysis of genome-wide DNA methylation during female germline development was used for confirmation. By pathway analysis and ... of early-stage female germ cells revealed by RNA sequencing of low-input cells and analysis of genome-wide DNA methylation.. Ma ... of early-stage female germ cells revealed by RNA sequencing of low-input cells and analysis of genome-wide DNA methylation ...
A nonparametric Bayesian approach for clustering bisulfate-based DNA methylation profiles | BMC Genomics | Full Text
Large-scale methylation arrays are now available for studying methylation genome-wide. The Illumina methylation platform ... Unique methylation patterns have been shown to exist in diseases including various types of cancer. DNA methylation analysis ... Cluster analysis is often used to identify DNA methylation subgroups for prognosis and diagnosis. However, due to the unique ... A Dirichlet process beta mixture model (DPBMM) is proposed that models the DNA methylation expressions as an infinite number of ...
Fabian Mueller | Stanford Medicine Profiles
Genome-wide DNA methylation analysis shows that CK2 primarily modulates CpG methylation of several repeats, most notably of Alu ... our data highlight that non-CpG methylation patterns reappear upon iPS cell reprogramming. Intriguingly, the patterns are ... Here we report a comprehensive analysis of non-CpG methylation in 76 genome-scale DNA methylation maps across pluripotent and ... and determined their genome-wide DNA methylation profiles. In addition to shared DNA methylation aberrations present in all our ...
DNA Methylation, Walter Doerfler (Volume editor) Petra Bohm (Volume editor) - Shop Online for Books in Australia
DNA Methylation: Development, Genetic Disease and Cancer (Current Topics in Microbiology and Immunology) by Walter Doerfler ( ... Volume editor) Petra Bohm (Volume editor)Buy . Books online: DNA Methylation: Development, Genetic Disease and Cancer (Current ... DNA Methylation Profiles of Female Steroid Hormone-driven Human Malignancies.- Genome-wide Analysis of DNA Methylation Changes ... It has become apparent that the genomes of many organisms are characterized by unique patterns of DNA methylation which can ...
Epigenomics chromatin biology therapeutics | Genetics | Cambridge University Press
Detection of CpG methylation patterns by affinity capture methods. 15. Genome-wide ChIP-DSL profiling of promoter methylation ... Cancer classification by genome-wide and quantitative DNA methylation analyses. 22. Promoter CpG island methylation in ... Advances in capillary electrophoresis-based methods for DNA methylation analysis. 19. Genome-wide methylome analysis based on ... Genome-wide DNA methylation analysis in patients with familial ATR-X mental retardation syndrome. 31. Kinases and phosphatases ...
Epigenetics in Melanoma | SpringerLink
Genome and transcriptome analyses and extensive studies in DNA methylation,... ... Tools and strategies for analysis of genome-wide and gene-specific DNA methylation patterns. Methods Mol Biol. 2017;1537:249-77 ... Genome-wide screen of promoter methylation identifies novel markers in melanoma. Genome Res. 2009;19(8):1462-70.PubMed ... Genome-wide methylation sequencing of paired primary and metastatic cell lines identifies common DNA methylation changes and a ...
Gene-set Analysis Is Severely Biased When Applied to Genome-Wide Methylation Data - PubMed
Genome-wide DNA methylation analysis revealed distinctive functional patterns for hyper-and hypo-methylation in treatment-naïve ... Gene-set Analysis Is Severely Biased When Applied to Genome-Wide Methylation Data Paul Geeleher 1 , Lori Hartnett, Laurance J ... Gene-set Analysis Is Severely Biased When Applied to Genome-Wide Methylation Data Paul Geeleher et al. Bioinformatics. 2013 ... Homeobox Gene Methylation in Lung Cancer Studied by Genome-Wide Analysis With a Microarray-Based Methylated CpG Island Recovery ...
Mesenchymal Stem Cells in Myeloid Malignancies: A Focus on Immune Escaping and Therapeutic Implications
Genome-wide DNA methylation analysis also showed globally altered DNA methylation pattern in AML MSCs. Generally, CpG ... As a matter of fact, recent studies demonstrated that leukemic MSCs harbor highly specific differences in methylation patterns ... Various alterations in cell adhesion, metabolism, cytokine signaling, autophagy, and methylation patterns of tumor-derived ... and methylation patterns, leading to and favoring differentiation arrest, proliferation, and clonal selection. Moreover, the ...
Max-Planck-Institut für Informatik: EpiExplorer and RnBeads: Integrative Analysis of Epigenomic Data
Various experimental assays have been developed for genome-wide analysis of DNA methylation patterns. RnBeads is a software ... Comprehensive analysis of DNA methylation data using RnBeads. DNA methylation comprises an important layer of epigenomic ... key strength lies in supporting exploratory hypothesis generation using a broad range of genome-wide data analyses performed in ... It is a major contributor to embryonic development, and aberrant methylation patterns have been associated with complex ...
DNA methylation analysis of the autistic brain reveals multiple dysregulated biological pathways | Translational Psychiatry
... have been suggested as molecular mechanism that can mediate the interaction between the environment and the genome to produce ... Here, using the Illumina 450 K methylation array we have determined the existence of many dysregulated CpGs in two cortical ... and that there is an inverse correlation between gene expression and DNA methylation within the individuals. Among these genes ... The central aim of this study is to determine the genome-wide DNA methylation patterns in autism brain and the significance of ...
Effects of genistein supplementation on genome‑wide DNA methylation and gene expression in patients with localized prostate...
Eisen MB, Spellman PT, Brown PO and Botstein D: Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad ... Differential methylation in genistein-treated tissue compared with placebo-treated tissue. The genome-wide DNA methylation ... Genome-wide DNA methylation arrays showed that a number of genes, including RBM28 and CYTSB, appeared to be demethylated in the ... Methylation data are available on GEO (accession number GSE84749).. Genome-wide expression profiling. Total RNA was extracted ...
Intermediate- and Low-Methylation Epigenotypes Do Not Correspond to CpG Island Methylator Phenotype (Low and -Zero) in...
Genome-wide methylation analysis of three epigenotypes. We carried out a comprehensive DNA methylation profiling of 21 DNA ... The DNA methylation pattern of these CpGs was further investigated by principal components analysis (PCA). As shown in Fig. 1A ... Using data gathered in genome-wide methylation analysis, we explored the methylation of 10 CpGs (B3GAT2, FOXL2, KCNK13, RAB31, ... Genome-scale methylation profiling of HME, IME, and LME DNA pools. A, principal components analysis of the methylation data of ...
Autism Research Database - Strategic Plan Objective Project Details | IACC
The primary tool for analysis will be DNA microarrays ("gene chips"), which allow a genome-wide scan.. ... Researchers will examine the methylation patterns of genes taken from post-mortem brain tissue of autistic individuals and ... DNA methylation and other epigenetic studies of autism brain , 43986 , 2010 , 2230. DNA methylation and other epigenetic ... One way that genes are turned off is through DNA methylation: an enzyme places a methyl group onto certain sequences of DNA, ...
Twin methodology in epigenetic studies | Journal of Experimental Biology
Souren et al., 2013) reported no significant intra-pair differential DNA methylation pattern in a genome-wide analysis. We are ... Adult monozygotic twins discordant for intra-uterine growth have indistinguishable genome-wide DNA methylation profiles. Genome ... 2004). Genetic analysis of genome-wide variation in human gene expression. Nature 430, 743-747. ... 2010). Changes in the pattern of DNA methylation associate with twin discordance in systemic lupus erythematosus. Genome Res. ...
Genome-Wide DNA Methylation Analysis. Total DNA was analyzed in all nonresponders (n = 6) and in the responders with the most ... A six months exercise intervention influences the genome-wide DNA methylation pattern in human adipose tissue. PLoS Genet 2013; ... D: Manhattan plot of the P values calculated from the genome-wide CpG site methylation analysis in HSkMCs (n = 491 sites across ... D: Manhattan plot of the P values calculated from the genome-wide CpG site methylation analysis in muscle tissue on all ...
EpigeneticsWhole genome bisulfiteDifferential MethylationAbstractRevealsAlterationsIdentified in embryonic stemHypermethylationAberrant DNA methylationBisulfite sequArabidopsisEpigenotypes of Latent Herpesvirus GenomesHypomethylationTranscriptionalBiolRegulation of Gene ExMammalian genomeChanges in DNA methylationSequenceWGBSGene regulationAllele-specific methylationHuman GenomeDifferentiationRole of DNA methylationLevels of DNA methylationStudies of DNA methylationEstablishment of DNA methylationTumorsOccursBioinformaticEvolutionaryMethylome450,000 CpG sitesPotential methylation sitesCancerEpigenomicSingle nucleotide pMechanismsDifferentially methylated regionsNucleotideHigh throughputIdentify DNA methylationRegions in the genomeMicroarrayDevelopmentalVariable DNA methylationDifferences in methylation
- Analysis of genome-wide profiles of DNA methylation (methylomes) in humans is revealing new associations between differentiation and DNA epigenetics [ 1 , 2 ]. (mdpi.com)
- A process called zygotic genome activation allows this to happen, and we're learning more about how epigenetics is involved. (activemotif.com)
Whole genome bisulfite5
- Whole-genome bisulfite sequencing (WGBS) represents a sensitive and robust method for the characterization of genome-wide methylation patterns at single-base resolution. (springer.com)
- Xi Y, Li W (2009) BSMAP: whole genome bisulfite sequence MAPping program. (springer.com)
- A systematic study of normalization methods for Infinium 450K methylation data using whole-genome bisulfite sequencing data. (upmc.edu)
- The RRBS method was first published in 2005, in the early days of NGS when sequencing was still expensive, as a way to get genome-wide single-nucleotide DNA methylation analysis for lower cost that whole genome bisulfite sequencing. (activemotif.com)
- There are also several genome-wide DNA methylation assays, such as reduced representation bisulfite sequencing (RRBS) and whole genome bisulfite sequencing (WGBS). (activemotif.com)
- DMAP: differential methylation analysis package for RRBS and WGBS data. (springer.com)
- Lyko F, Foret S, Kucharski R, Wolf S, Falckenhayn C, Maleszka R (2010) The honey bee epigenomes: differential methylation of brain DNA in queens and workers. (springer.com)
- We found that ALL cells displayed highly divergent DNA methylation patterns depending on their cytogenetic subtype and widespread regions of differential methylation were enriched for repressive histone marks. (avhandlingar.se)
- The differential methylation pattern of crown galls and the stem tissue from which they originate correlated with transcriptional changes. (uni-wuerzburg.de)
- Akalin A, Garrett-Bakelman FE, Kormaksson M et al (2012a) Base-pair resolution DNA methylation sequencing reveals profoundly divergent epigenetic landscapes in acute myeloid leukemia. (springer.com)
- Cokus SJ, Feng S, Zhang X et al (2008) Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. (springer.com)
- Whole genome methylation sequencing reveals distinct impact of differential methylations on gene transcription in prostate cancer. (upmc.edu)
- Genome-wide methylation analysis reveals that each pituitary adenoma subtype displays a disease-specific DNA methylation pattern. (aacrjournals.org)
- Mllt10 knockout mouse model reveals critical role of Af10-dependent H3K79 methylation in midfacial development. (abcam.com)
- Various alterations in cell adhesion, metabolism, cytokine signaling, autophagy, and methylation patterns of tumor-derived mesenchymal stem cells have been demonstrated, contributing to the genesis of a leukemic permissive niche. (hindawi.com)
- This highlights the importance of analyzing methylation status, as looking at genetic sequence alone may not provide the complete picture on heritable DNA alterations. (sfari.org)
- Documenting epigenetic alterations (DNA methylation and miRNA) in cancer progression (primary to metastasis) and the test the functional consequences of these changes in the laboratory. (otago.ac.nz)
- Alterations of methylation in DNA from human lung cancer tissues. (cdc.gov)
- Alterations in DNA methylation have been associated with cancers at almost all tumor sites and represent one of the most consistent changes in neoplastic cells. (cdc.gov)
- Epigenetic control of gene expression lasts through multiple cell divisions without alterations in primary DNA sequence and can occur via mechanisms that include histone modification and DNA methylation. (stanford.edu)
- A feature of various human diseases including cancer is genome-wide alterations in DNA methylation content. (activemotif.com)
- Here, by performing a genome-wide methylation analysis, we identified several CLL-specific methylation alterations. (oncotarget.com)
Identified in embryonic stem2
- Nearly one-quarter of all methylation identified in embryonic stem cells was in a non-CG context, suggesting that embryonic stem cells may use different methylation mechanisms to affect gene regulation. (psu.edu)
- 5-mC generally occurs on cytosine bases that are followed by guanines, which are referred to as "CpGs", although non-CpG methylation has been identified in embryonic stem cells 2 . (activemotif.com)
- Currently, relatively little is known about specific patterns of CpG island hypermethylation in ICC. (aacrjournals.org)
- The two major types of methylation include hypomethylation and hypermethylation. (biomedcentral.com)
- Subgroup analysis showed that FLI1 hypermethylation in both tissue and plasma samples was associated with liver metastasis in MSI−/EBV− GC, and MSC hypermethylation in tissue samples was correlated with liver metastasis in MSI+ or EBV+ GC. (biomedcentral.com)
- By conducting next-generation sequencing-based DNA methylome analysis, we have discovered marked hypermethylation at the promoter of the major cellular cholesterol efflux transporter, ABCA1 , in LNCaP prostate cancer cells. (aacrjournals.org)
Aberrant DNA methylation3
- It is unknown whether aberrant DNA methylation can cause neurodegeneration. (jneurosci.org)
- Aberrant DNA methylation is involved in gastric carcinogenesis and may serve as a useful biomarker in the diagnosis and detection of gastric cancer (GC) recurrence. (biomedcentral.com)
- Aberrant DNA methylation has been strongly associated with progression, relapse, and drug resistance. (bloodjournal.org)
- Asselman J (2018) Bioinformatic analysis of methylation patterns using bisulfite sequencing data. (springer.com)
- Efficient and user-friendly tools are critical in carrying out such analysis on high-throughput bisulfite sequencing data. (biomedcentral.com)
- In conclusion, BSPAT is an efficient and convenient tool for high-throughput bisulfite sequencing data analysis that can be broadly used. (biomedcentral.com)
- Along with the generation of bisulfite sequencing data, many bisulfite sequencing data analysis tools have been proposed in recent years. (biomedcentral.com)
- Dinh HQ, Dubin M, Sedlazeck FJ et al (2012) Advanced methylome analysis after bisulfite deep sequencing: an example in Arabidopsis. (springer.com)
- To investigate whether DNA methylation plays a role in heterosis, we compared at single-base-pair resolution the DNA methylomes of Arabidopsis thaliana Landsberg erecta and C24 parental lines and their reciprocal F1 hybrids that exhibited heterosis. (plantcell.org)
- We previously showed that Arabidopsis thaliana plants with mutations in the H3K4m2/m3 demethylase JUMONJI 14 (JMJ14) exhibit a mild reduction in RNA-directed DNA methylation (RdDM) that is associated with an increase in H3K4m2/m3 levels. (diagenode.com)
- In this study, the methylation pattern of Arabidopsis thaliana crown galls was analyzed on a genome-wide scale as well as at the single gene level. (uni-wuerzburg.de)
- Draft genome of the \(Arabidopsis\) \(thaliana\) phyllosphere bacterium, \(Williamsia\) sp. (uni-wuerzburg.de)
- Here, we generated a genome expression atlas of 18 organ or tissue types representing the life cycle of Arabidopsis ( Arabidopsis thaliana ). (plantphysiol.org)
- In addition, we also examined the light-responsive expression of the Arabidopsis genome among the three organs of seedlings. (plantphysiol.org)
- Several interesting insights on the regulation of genome expression during Arabidopsis development and its response to light were observed. (plantphysiol.org)
Epigenotypes of Latent Herpesvirus Genomes1
- We discovered increased frequency of hypomethylation across the genome after reloading (18,816 CpGs) versus earlier loading (9,153 CpG sites). (nature.com)
- In this study, a bias towards hypomethylation in males was dependent on testosterone exposure during puberty, which was coincident with loss of methylation. (biomedcentral.com)
- The reduced levels of DNA methylation in endosperm are caused by hypomethylation of the maternal allele for both MEGs and PEGs in all cases tested. (plantcell.org)
- DNA methylation is the paradigm epigenetic modification that is associated with transcriptional repression. (springer.com)
- We apply a novel analytical approach to measure and compare transcriptional and epigenetic variability genome-wide across CD14 + CD16 − monocytes, CD66b + CD16 + neutrophils, and CD4 + CD45RA + naïve T cells from the same 125 healthy individuals. (biomedcentral.com)
- In order to determine the evolutionary conservation of DNA methylation patterns and transcriptional regulatory programs in the placenta, we performed a genome-wide methylome (MethylC-seq) analysis of human, rhesus macaque, squirrel monkey, mouse, dog, horse, and cow placentas as well as opossum extraembryonic membrane. (nih.gov)
- Induction of dedifferentiation, genomewide transcriptional programming, and epigenetic reprogramming by extracts of carcinoma and embryonic stem cells. (uio.no)
- Finally, RNA sequencing analyses indicate that at RdDM targets, the increase of H3K4m2/m3 is not generally associated with transcriptional de-repression. (diagenode.com)
Regulation of Gene Ex4
- Background: DNA methylation primarily occurs at CpG dinucleotides in mammals and is a common epigenetic mark that plays a critical role in the regulation of gene expression. (garvan.org.au)
- Jaenisch R, Bird A (2003) Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals. (springer.com)
- The spatial organization of the human genome within the nucleus plays important roles in the regulation of gene expression and other cellular processes. (activemotif.com)
- The precise mechanisms for this transformation are not well defined, however recent studies suggest that aberrant regulation of gene expression or DNA methylation may play an important role. (avhandlingar.se)
Changes in DNA methylation3
- Causes and Consequences of Age-Related Changes in DNA Methylation: A Role for ROS? (mdpi.com)
- Changes in DNA methylation between primary and recurrent tumors were extremely variable, and no consistent DNA methylation changes were found. (eur.nl)
- Changes in DNA methylation patterns have also been implicated in the pathogenesis of many human diseases. (dcu.ie)
- But most existing algorithms working on methylation data are from sequence level. (biomedcentral.com)
- DNA methylation (DNAm), a reversible chemical modification of DNA, is a way for cells to regulate their gene expression program without changing their DNA sequence. (autismspeaks.org)
- Methylation on cytosine can occur in different sequence contexts but largely in a CpG dinucleotide context ( Fazzari and Greally 2004 ). (g3journal.org)
- Methylation can change the activity of a DNA segment without changing the sequence. (wikipedia.org)
- In plants and other organisms, DNA methylation is found in three different sequence contexts: CG (or CpG ), CHG or CHH (where H correspond to A, T or C). In mammals however, DNA methylation is almost exclusively found in CpG dinucleotides, with the cytosines on both strands being usually methylated. (wikipedia.org)
- Furthermore, non-CpG methylation has also been observed in hematopoietic progenitor cells, and it occurred mainly in a CpApC sequence context. (wikipedia.org)
- To further reveal the genome-wide methylation pattern, MeDIP-Seq reads distribution were analyzed in 2 kb region upstream of the transcription start sites (TSS), 5'-UTRs, coding DNA sequence (CDS), introns, 3'-UTRs, 2 kb region downstream of the transcription termination site (TTS) and repeats (Figure 2). (thefreedictionary.com)
- Here we describe the general physiological features of this microorganism together with the draft genome sequence and annotation. (uni-wuerzburg.de)
- For example, ultra-deep bisulfite sequencing is designed to sequence a limited number of loci but with an extreme high coverage [ 5 , 6 ], which makes analysis of methylation co-occurrence patterns feasible. (biomedcentral.com)
- Here, we describe a step-by-step protocol for the generation and analysis of WGBS datasets using standard Illumina sequencing platforms. (springer.com)
- In comparison to whole-genome sequencing, WGBS has additional caveats that require particular attention and are highlighted in this chapter. (springer.com)
- DNA methylation is a fundamental epigenetic mark known to have wide-ranging effects on gene regulation in a variety of animal taxa. (pubmedcentralcanada.ca)
- An epigenetic modification associated with gene regulation, DNA methylation plays a key role in a wide variety of biological processes. (dcu.ie)
- Bisulfite-converted DNA can be analyzed for gene-or allele-specific methylation patterns by amplification with primers that differentiate between methylated and unmethylated (converted) sequences, or by performing Sanger sequencing of the amplified regions. (activemotif.com)
- It has also reported some interesting methylation co-occurrence patterns and a potential allele-specific methylation case. (biomedcentral.com)
- The role of CpG island methylation in normal development and cell differentiation is of keen interest, but remains poorly understood. (nih.gov)
- Non-CG methylation disappeared upon induced differentiation of the embryonic stem cells, and was restored in induced pluripotent stem cells. (psu.edu)
- Many studies have mapped DNA methylation changes associated with embryogenesis, cell differentiation, and cancer at a genome-wide scale. (g3journal.org)
- This approach has the final goal of dissecting the molecular processes that mediate methylation changes in the morphogenesis and differentiation of the normal breast and to identify "hot spot" loci for gene silencing in breast carcinogenesis. (yu.edu)
- DNA methylation is involved in immune cell differentiation and identity. (biomedcentral.com)
- Through this analysis, the researchers were able to identify a unique Th17-specific epigenetic signature and reinforce the finding that Th cell differentiation is associated with major epigenetic changes. (zymoresearch.com)
Role of DNA methylation1
Levels of DNA methylation1
- Children with a record of hospitalisation for severe RSV bronchiolitis demonstrated markedly lower levels of DNA methylation at two cytosine-phosphate-guanine dinucleotide (CpG) loci of the PRF1 proximal enhancer, corresponding to a signal transducer and activator of transcription 5 (STAT5) responsive element, compared to controls, adjusted odds ratios of 0.82 (95% confidence interval [CI] 0.71, 0.94) and 0.73 (95% CI 0.58, 0.92) for each 1% increase in DNA methylation. (biomedcentral.com)
Studies of DNA methylation1
Establishment of DNA methylation2
- Proper establishment of DNA methylation early in embryogenesis is vital for normal development in many organisms ( Law and Jacobsen 2010 ). (g3journal.org)
- We use various mouse models to investigate early nutritional influences on the developmental establishment of DNA methylation and associated phenotypes. (wur.nl)
- We analyzed DNA methylation profiles of the digestive tract surface and the central bulk and invasive front regions of colorectal tumors.We determined the DNA methylation profiles of >450,000 CpG sites in 3 macrodissected regions of 79 colorectal tumors and 23 associated liver metastases, obtained from 2 hospitals in Spain. (stanford.edu)
- A supervised cluster analysis based on differentially expressed microRNAs between paired primary and recurrent WDLPS did not reveal a clear cluster pattern separating the primary from the recurrent tumors. (eur.nl)
- As a result, a supervised clustering analysis based on DMRs between primary and recurrent tumors did not show a distinct cluster pattern based on any of the features. (eur.nl)
- Subgroup analysis for tumors localized in the extremity or the retroperitoneum also did not yield a clear distinction between primary and recurrent WDLPS samples. (eur.nl)
- Crown gall tumors develop after integration of the T-DNA of virulent Agrobacterium tumefaciens strains into the plant genome. (uni-wuerzburg.de)
- Moreover, laboratory experiments exploring evolutionary mechanisms that allow rapid adaptation to contaminants (e.g., fluctuation analysis or ratchet procedures) have proven to be useful linking concentration of pollutants and adaptation strategy. (omicsonline.org)
- Zemach A, McDaniel IE, Silva P, Zilberman D (2010) Genome-wide evolutionary analysis of eukaryotic DNA methylation. (springer.com)
- High CpG methylation in mammalian genomes has an evolutionary cost because it increases the frequency of spontaneous mutations. (wikipedia.org)
- Moreover, the inferred patterns of methylation can be used to test current hypotheses explaining the evolutionary persistence of DNA methylation ( Yi and Goodisman 2009 ). (pubmedcentralcanada.ca)
- We used a meta-epigenomic approach that combines DNA methylation profiles across many small pools of cells and performed single-cell methylome sequencing to assess cell-to-cell heterogeneity. (stanford.edu)
- Further methylome analysis through methylation sensitive high-resolution melting (MS-HRM) and pyrosequencing demonstrated that CD4+ T cells share more demethylated regions with Th17 cells when compared to Th1 cells, and that overall Th17 cells display the highest number of demethylated regions. (zymoresearch.com)
450,000 CpG sites1
Potential methylation sites1
- Perturbations of DNA methylation patterns are frequently associated with cancer and aging, raising a great interest in understanding the contribution of this mark to human health. (springer.com)
- Unique methylation patterns have been shown to exist in diseases including various types of cancer. (biomedcentral.com)
- DNA methylation analysis promises to become a powerful tool in cancer diagnosis, treatment and prognostication. (biomedcentral.com)
- Decreased Fidelity in Replicating DNA Methylation Patterns in Cancer Cells Leads to Dense Methylation of a CpG Island. (fishpond.com.au)
- We demonstrate this bias using published data from a study of differential CpG island methylation in lung cancer and a dataset we generated to study methylation changes in patients with long-standing ulcerative colitis. (nih.gov)
- Accounting for the bias in the lung cancer and ulcerative colitis datasets provides novel biological insights into the role of methylation in cancer development and chronic inflammation, respectively. (nih.gov)
- De novo methylation of CpG islands is a common phenomenon in human cancer, but the mechanisms of cancer-associated DNA methylation are not known. (nih.gov)
- DNA methylation as part of the epigenetic gene-silencing complex is a universal occurring change in lung cancer. (nih.gov)
- It is a major contributor to embryonic development, and aberrant methylation patterns have been associated with complex diseases like cancer. (mpg.de)
- Cancer genome landscapes. (springer.com)
- Kulis M, Esteller M. DNA methylation and cancer. (springer.com)
- Therefore, DNA methylation is an ideal target for cancer diagnosis in clinical practice [ 6 , 7 ]. (biomedcentral.com)
- The non-invasive nature of cfDNA methylation profiling makes it a promising strategy for general cancer screening. (biomedcentral.com)
- This detailed analysis revealed that both enrichment techniques are sensitive for detecting DMRs and preferentially identified different CpG rich regions of the prostate cancer genome, with MeDIP commonly enriching for methylated regions with a low CpG density, while MBD capture favours regions of higher CpG density and identifies the greatest proportion of CpG islands. (garvan.org.au)
- The Cancer Genome Atlas (TCGA) [ 9 ] classifies GC into four types: (1) Epstein-Barr virus positive (EBV+), (2) microsatellite instability-high (MSI+), (3) genomically stable, and (4) chromosomal instability. (biomedcentral.com)
- 2) Project title: Analysis of cancer genome atlas data to identify epigenetic signature of tumour metastatis. (otago.ac.nz)
- To determine if global methylation may contribute to the development of lung cancer, we studied genome-wide aberrant methylation pattern in 57 lung cancer cases and matched controls. (cdc.gov)
- What Can Histone Methylation Patterns in Kidney Cancer Teach Us About Disease Progression & New Treatments Options? (activemotif.com)
- NNMT promotes epigenetic remodeling in cancer by creating a metabolic methylation sink. (abcam.com)
- In the Murphy laboratory, we use the zebrafish model, mammalian stem cells, and human cancer cell lines, to investigate how epigenetic marks control gene expression patterns, and drive cell state transitions. (rochester.edu)
- We had previously developed highly sensitive DNA methylation detection to diagnose lung cancer in patients with pulmonary nodules. (biomedcentral.com)
- The researchers carried out several types of genome-wide methylation analyses on the cells, looking for epigenomic differences that would suggest environmental influences at work. (psychcentral.com)
- Continue to develop tools, statistical methods for accurate analysis of epigenomic datasets from next generation sequencing technologies (NGS). (otago.ac.nz)
- Recent years saw great progress in miniaturization of genome-wide epigenomic profiling, enabling large-scale epigenetic biomarker screens for disease diagnosis, prognosis, and stratification on patient-derived samples. (fluidigm.com)
- In this review we provide an overview of current genome-wide epigenomic profiling technologies and main technological advances that allowed miniaturization of these assays down to single-cell level. (fluidigm.com)
- Whole blood transcriptome and epigenomic patterns were assessed by microarray-based, genome-wide technologies. (bvsalud.org)
Single nucleotide p3
- Whole Genome Single Nucleotide Polymorphism Array Analysis is Complementary to Classical Cytogenetic Analysis in the Evaluation of Lymphoid Proliferations. (upmc.edu)
- In the second study we used technology developed for large-scale single nucleotide polymorphism (SNP) genotyping for quantitative analysis of allele-specific gene expression (ASE), revealing widespread ASE in ALL cells. (avhandlingar.se)
- Objectives: To identify gene-environment interaction effects on childhood asthma using genome-wide single-nucleotide polymorphism (SNP) data and air pollution exposure. (uni-muenchen.de)
- High throughput technologies reveal epigenetic mechanisms at a genome-wide level, giving rise to epigenomics as a new discipline with a distinct set of research questions and methods. (cambridge.org)
- The extensive coverage of current theory, new technologies, and disease mechanisms, all associated with epigenomics, makes this book invaluable to students and researchers in a wide range of disciplines. (cambridge.org)
- Of the different mechanisms, DNA methylation is the most robust form of epigenetic modification readily measurable using high-throughput techniques. (biologists.org)
- Thus, motor neurons can engage epigenetic mechanisms to drive apoptosis, involving Dnmt upregulation and increased DNA methylation. (jneurosci.org)
- With the advent of large-scale analytical methods to document the genome, epigenome, proteome, and metabolome, new opportunities have arisen to uncover the mechanisms generating heterosis. (plantphysiol.org)
- Epigenetic mechanisms are established during development to stably regulate tissue-specific patterns of gene expression. (wur.nl)
- However, the survival mechanisms of tardigrades are still poorly understood mainly due to the absence of detailed knowledge about the proteome and genome of these organisms. (uni-wuerzburg.de)
- Genotype-dependent methylation may account, in part, for the mechanisms underlying observed G×E interactions in APOE, IL6, and ABCA1. (tufts.edu)
Differentially methylated regions2
- Genome-wide DNA methylation and differentially methylated regions (DMRs) were assessed by methylated DNA sequencing (MeD-seq). (eur.nl)
- Using a genome-wide, array-based method of analysis on a subset of the cohort (n=6) from the RCT, we identified 5 novel folate-sensitive differentially methylated regions (FS-DMRs): Inosital hexakisphosphate kinase 1 (IP6K1), Chromosome 9 Open Reading Frame 44 (Chr9ORF44), RAS p21 protein activator 4 (RASA4), Sphingosine-1-phosphate lyase 1 (SPGL1) and Chromosome 19 Open Reading Frame 75 (Chr19ORF75). (dcu.ie)
- I performed the first genome-wide study to provide single-nucleotide resolution DNA methylation profiles in human neutrophils and showed existence of wide-spread inter-individual variation in epigenetic marks in normal population. (otago.ac.nz)
- The 96-well assay utilizes a unique hybridization approach that quantitates 5-mC levels of Long Interspersed Nucleotide Element 1 (LINE-1) repeats as a surrogate measure for global DNA methylation. (activemotif.com)
- Bisulfite sequencing is one of the most popular methods, which uses bisulfite treated DNA samples to obtain single nucleotide methylation status. (biomedcentral.com)
- Then, the PIK3R1 gene was selected for further RT-qPCR analysis and cytosine-guanine nucleotide (CpG) sites methylation evaluation. (bvsalud.org)
- Here, we present an in-depth analysis of 54 single-CpG-resolution DNA methylomes of normal human cell types by integrating high-throughput sequencing-based methylation data. (g3journal.org)
- He is the Director of the High Throughput Genome Center at the Department of Pathology, University of Pittsburgh, involving collaboration of faculties from multiple departments. (upmc.edu)
- This integrated analysis, of 3 high throughput platforms, suggests that although multiple defects evolve from diagnosis to relapse, some may converge on distinct pathways, such as the WNT and mitogen-activated protein kinase signaling pathways. (bloodjournal.org)
Identify DNA methylation2
- Here we discuss commonly used wet-lab methodologies and computational approaches to identify DNA methylation patterns and measure their dynamics during biological processes in a quantitative and unbiased manner. (springer.com)
- Cluster analysis is often used to identify DNA methylation subgroups for prognosis and diagnosis. (biomedcentral.com)
Regions in the genome1
- DNA methylation levels at distinct regions in the genome were substantially increased at relapse compared to matched cells from diagnosis.Collectively, the results presented in this thesis provide new insights into the patterns of gene expression and epigenetic changes in ALL and further increase our understanding of the development and progression of the disease, which will hopefully lead to better treatment options in the future. (avhandlingar.se)
- Our understanding of genome-wide DNA methylation changes in a developmental or disease-related context has been steadily growing. (g3journal.org)
- Here, we characterize genome-wide methylation at a base-pair resolution, and compare these results to gene expression across five developmental stages and to methylation patterns reported in other insects. (lu.se)
- We speculate that loss of methylation may result in increased developmental specialization in evolution and acquisition of methylation may lead to broader constitutive expression. (lu.se)
- The development of complex eukaryotic organisms can be viewed as the selective expression of distinct fractions of the genome in different organs or tissue types in response to developmental and environmental cues. (plantphysiol.org)
- Higher plants possess a relatively simple developmental process, with only three nonreproductive organ systems and fewer than 25 major tissue and cell types ( Eeau, 1977 ), thereby providing a good model for defining the organ- and tissue-specific genome expression patterns during development. (plantphysiol.org)
Variable DNA methylation2
- We categorized the 26,000,000 human autosomal CpGs based on their methylation levels across multiple cell types to identify variably methylated CpGs and found that 22.6% exhibited variable DNA methylation. (g3journal.org)
- This work provides a comprehensive resource for understanding the nature and mechanism of variable phenotypic traits and altered disease susceptibility due to variable DNA methylation patterns and also has broader implications for the selection of DNA methylation based biomarker. (otago.ac.nz)